HEADER RNA BINDING PROTEIN 17-DEC-20 7BBB TITLE SOLUTION STRUCTURE OF C-TERMINAL RECA AND RRM DOMAINS OF THE DEAD BOX TITLE 2 HELICASE DBPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DBPA; COMPND 3 CHAIN: A; COMPND 4 EC: 3.6.4.13; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TWO NONNATIVE GLYCINE RESIDUES WERE INTRODUCED AT THE COMPND 7 N-TERMINUS DURING THE CLONING PROCEDURE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 GENE: DBPA, B1343, JW1337; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DEAD BOX HELICASE, RIBOSOME BIOGENESIS, RNA, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.P.WURM,R.SPRANGERS REVDAT 3 14-JUN-23 7BBB 1 REMARK REVDAT 2 22-SEP-21 7BBB 1 JRNL REVDAT 1 14-JUL-21 7BBB 0 JRNL AUTH J.P.WURM,K.A.GLOWACZ,R.SPRANGERS JRNL TITL STRUCTURAL BASIS FOR THE ACTIVATION OF THE DEAD-BOX RNA JRNL TITL 2 HELICASE DBPA BY THE NASCENT RIBOSOME. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34453003 JRNL DOI 10.1073/PNAS.2105961118 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.5 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BBB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292103734. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 290 REMARK 210 PRESSURE : AMBIENT PA REMARK 210 SAMPLE CONTENTS : 0.8 MM U-2H;U-15N;NA REMARK 210 -Y;METHYL13C1H-ILMVAT DBPA RESIDUES 209-457, 20 MM ARGININE/ REMARK 210 GLUTAMATE, 20 MM HEPES, 250 MM NACL, 1 MM DTT, 95% H2O/5% D2O; REMARK 210 0.8 MM U-2H;U-15N;NA-Y;METHYL13C1H-ILMVAT DBPA RESIDUES 209-457, REMARK 210 20 MM ARGININE/GLUTAMATE, 20 MM HEPES, 250 MM NACL, 1 MM DTT, REMARK 210 100% D2O; 0.74 MM [U-10% 13C] DBPA RESIDUES 209-457, 20 MM REMARK 210 ARGININE/GLUTAMATE, 20 MM HEPES, 250 MM NACL, 1 MM DTT, 100% D2O; REMARK 210 0.8 MM U-2H;U-15N;METHYL13C1H-ILMVA DBPA RESIDUES 209-457, 20 REMARK 210 MM ARGININE/GLUTAMATE, 20 MM HEPES, 250 MM NACL, 1 MM DTT, 95% REMARK 210 H2O/5% D2O; 0.74 MM U-13C; U-15N; U-2H;U-13C/U-2H/METHYL-1H ILV REMARK 210 DBPA RESIDUES 209-457, 20 MM ARGININE/GLUTAMATE, 20 MM HEPES, REMARK 210 250 MM NACL, 1 MM DTT, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNH NOESY; 3D HNCACB; 3D REMARK 210 HNCO; 3D HN(COCA)CB; 3D HN(CA)CO; REMARK 210 3D H(CCO)NH; 3D CCH NOESY; 3D REMARK 210 HCH NOESY; 3D CNH NOESY; 2D 1H- REMARK 210 13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, NMRFAM-SPARKY 1.414 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 SER A 209 -70.84 -39.53 REMARK 500 1 ALA A 212 65.75 39.93 REMARK 500 1 LEU A 213 149.99 -36.52 REMARK 500 1 ALA A 302 37.79 -92.56 REMARK 500 1 LEU A 305 -170.62 -61.62 REMARK 500 1 LYS A 308 33.46 -145.28 REMARK 500 1 SER A 309 30.65 -164.00 REMARK 500 1 ALA A 319 -174.43 -58.38 REMARK 500 1 ARG A 334 39.10 -155.80 REMARK 500 1 SER A 338 -167.87 -103.72 REMARK 500 1 CYS A 345 145.64 179.33 REMARK 500 1 ALA A 346 165.26 -48.62 REMARK 500 1 ASN A 365 76.91 -101.43 REMARK 500 1 TRP A 366 95.95 -59.23 REMARK 500 1 ALA A 383 118.25 -160.60 REMARK 500 1 ASP A 388 37.39 -94.55 REMARK 500 1 PRO A 397 68.61 -69.85 REMARK 500 1 LYS A 445 156.23 178.49 REMARK 500 2 ALA A 212 -172.98 -177.56 REMARK 500 2 PRO A 215 -168.05 -69.75 REMARK 500 2 ILE A 216 105.10 -56.67 REMARK 500 2 LYS A 308 34.10 -175.37 REMARK 500 2 SER A 309 29.58 -162.40 REMARK 500 2 ALA A 319 167.53 -49.26 REMARK 500 2 SER A 338 -87.08 -154.61 REMARK 500 2 CYS A 345 179.08 179.21 REMARK 500 2 ASN A 365 63.10 -115.57 REMARK 500 2 PRO A 370 -170.28 -69.76 REMARK 500 2 ASP A 388 30.88 -95.13 REMARK 500 2 PRO A 397 75.06 -69.75 REMARK 500 3 THR A 210 105.95 -160.27 REMARK 500 3 LEU A 305 -177.82 -65.14 REMARK 500 3 SER A 309 35.51 -171.93 REMARK 500 3 ALA A 319 -175.79 -56.99 REMARK 500 3 ARG A 334 53.36 -175.42 REMARK 500 3 CYS A 345 151.66 178.88 REMARK 500 3 ASN A 365 78.48 -105.90 REMARK 500 3 PRO A 370 -173.21 -69.65 REMARK 500 3 SER A 373 -74.57 -100.56 REMARK 500 3 SER A 374 143.36 -175.53 REMARK 500 3 ASP A 388 31.27 -92.66 REMARK 500 3 PRO A 397 75.15 -69.80 REMARK 500 4 LEU A 305 -176.70 -63.79 REMARK 500 4 SER A 309 34.61 -170.46 REMARK 500 4 ALA A 319 178.75 -55.33 REMARK 500 4 ARG A 334 49.76 -146.76 REMARK 500 4 CYS A 345 145.81 178.09 REMARK 500 4 ASN A 365 69.32 -110.02 REMARK 500 4 ALA A 371 -48.05 -135.98 REMARK 500 4 SER A 374 75.33 -101.30 REMARK 500 REMARK 500 THIS ENTRY HAS 237 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50356 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS REMARK 900 RELATED ID: 34584 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF C-TERMINAL RECA AND RRM DOMAINS OF THE DEAD REMARK 900 BOX HELICASE DBPA DBREF 7BBB A 209 457 UNP P21693 DBPA_ECOLI 209 457 SEQADV 7BBB GLY A 207 UNP P21693 CLONING ARTIFACT SEQADV 7BBB GLY A 208 UNP P21693 CLONING ARTIFACT SEQRES 1 A 251 GLY GLY SER THR ASP ALA LEU PRO PRO ILE GLU GLN GLN SEQRES 2 A 251 PHE TYR GLU THR SER SER LYS GLY LYS ILE PRO LEU LEU SEQRES 3 A 251 GLN ARG LEU LEU SER LEU HIS GLN PRO SER SER CYS VAL SEQRES 4 A 251 VAL PHE CYS ASN THR LYS LYS ASP CYS GLN ALA VAL CYS SEQRES 5 A 251 ASP ALA LEU ASN GLU VAL GLY GLN SER ALA LEU SER LEU SEQRES 6 A 251 HIS GLY ASP LEU GLU GLN ARG ASP ARG ASP GLN THR LEU SEQRES 7 A 251 VAL ARG PHE ALA ASN GLY SER ALA ARG VAL LEU VAL ALA SEQRES 8 A 251 THR ASP VAL ALA ALA ARG GLY LEU ASP ILE LYS SER LEU SEQRES 9 A 251 GLU LEU VAL VAL ASN PHE GLU LEU ALA TRP ASP PRO GLU SEQRES 10 A 251 VAL HIS VAL HIS ARG ILE GLY ARG THR ALA ARG ALA GLY SEQRES 11 A 251 ASN SER GLY LEU ALA ILE SER PHE CYS ALA PRO GLU GLU SEQRES 12 A 251 ALA GLN ARG ALA ASN ILE ILE SER ASP MET LEU GLN ILE SEQRES 13 A 251 LYS LEU ASN TRP GLN THR PRO PRO ALA ASN SER SER ILE SEQRES 14 A 251 ALA THR LEU GLU ALA GLU MET ALA THR LEU CYS ILE ASP SEQRES 15 A 251 GLY GLY LYS LYS ALA LYS MET ARG PRO GLY ASP VAL LEU SEQRES 16 A 251 GLY ALA LEU THR GLY ASP ILE GLY LEU ASP GLY ALA ASP SEQRES 17 A 251 ILE GLY LYS ILE ALA VAL HIS PRO ALA HIS VAL TYR VAL SEQRES 18 A 251 ALA VAL ARG GLN ALA VAL ALA HIS LYS ALA TRP LYS GLN SEQRES 19 A 251 LEU GLN GLY GLY LYS ILE LYS GLY LYS THR CYS ARG VAL SEQRES 20 A 251 ARG LEU LEU LYS HELIX 1 AA1 GLY A 227 GLN A 240 1 14 HELIX 2 AA2 THR A 250 GLY A 265 1 16 HELIX 3 AA3 GLU A 276 ASN A 289 1 14 HELIX 4 AA4 ASP A 321 ALA A 333 1 13 HELIX 5 AA5 ALA A 346 GLU A 348 5 3 HELIX 6 AA6 GLU A 349 LEU A 360 1 12 HELIX 7 AA7 GLY A 390 LYS A 394 5 5 HELIX 8 AA8 GLY A 398 THR A 405 1 8 HELIX 9 AA9 GLN A 431 GLY A 443 1 13 SHEET 1 AA1 7 ALA A 268 LEU A 271 0 SHEET 2 AA1 7 VAL A 294 ALA A 297 1 O VAL A 296 N LEU A 271 SHEET 3 AA1 7 CYS A 244 PHE A 247 1 N CYS A 244 O LEU A 295 SHEET 4 AA1 7 LEU A 312 ASN A 315 1 O VAL A 314 N PHE A 247 SHEET 5 AA1 7 LEU A 340 PHE A 344 1 O PHE A 344 N ASN A 315 SHEET 6 AA1 7 GLU A 217 TYR A 221 1 N GLN A 219 O ALA A 341 SHEET 7 AA1 7 ASN A 365 GLN A 367 1 O GLN A 367 N PHE A 220 SHEET 1 AA2 3 MET A 382 ILE A 387 0 SHEET 2 AA2 3 VAL A 425 ARG A 430 -1 O VAL A 425 N ILE A 387 SHEET 3 AA2 3 ILE A 415 VAL A 420 -1 N LYS A 417 O ALA A 428 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1